Variant report

Variant	rs1992569
Chromosome Location	chr4:99806626-99806627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99805865..99807821-chr4:99847875..99849598,2	MCF-7	breast:
2	chr4:99800676..99802842-chr4:99806350..99809597,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1154412	1.00[ASN][1000 genomes]
rs11722494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727079	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727086	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731092	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107892	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115072	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115688	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127259	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130454	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13832	1.00[ASN][1000 genomes]
rs17511498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17583053	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004994	1.00[ASN][1000 genomes]
rs2230574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018048	1.00[ASN][1000 genomes]
rs34073334	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34116542	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164768	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34445885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34552530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34849916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35360485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35619083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885444	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36061550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699689	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699692	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323189	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323190	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323206	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67650226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692635	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7688221	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688461	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896992	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99792400-99825000	Weak transcription	Gastric	stomach
2	chr4:99795000-99807000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:99796000-99826400	Weak transcription	Right Ventricle	heart
4	chr4:99796600-99806800	Weak transcription	HSMMtube	muscle
5	chr4:99796600-99807600	Weak transcription	Brain Germinal Matrix	brain
6	chr4:99796800-99814400	Weak transcription	Fetal Brain Male	brain
7	chr4:99797000-99807200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:99797000-99826600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:99797200-99806800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:99797400-99813400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:99797400-99813400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:99797400-99815200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:99798400-99823000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:99798600-99824400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:99799000-99823000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:99799200-99806800	Weak transcription	Brain Substantia Nigra	brain
17	chr4:99799400-99807000	Weak transcription	A549	lung
18	chr4:99799400-99807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:99799800-99811800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:99799800-99823200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:99800000-99811000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:99800000-99815000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:99800200-99813200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:99800200-99823400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:99800400-99823200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:99800600-99824200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:99800800-99813400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:99801400-99814400	Weak transcription	Psoas Muscle	Psoas
29	chr4:99801600-99829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:99802000-99808400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:99802200-99808600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:99802200-99809400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:99802200-99815200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:99802200-99824000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:99802400-99811400	Strong transcription	HMEC	breast
36	chr4:99802400-99812200	Strong transcription	Liver	Liver
37	chr4:99802400-99812800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:99802400-99814200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:99802600-99808800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:99802600-99811600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:99802600-99812800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:99802600-99813200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:99802600-99823800	Strong transcription	Fetal Thymus	thymus
44	chr4:99802600-99824400	Strong transcription	Dnd41	blood
45	chr4:99802800-99808000	Strong transcription	Fetal Intestine Large	intestine
46	chr4:99802800-99808400	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:99802800-99819600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:99802800-99824600	Weak transcription	Pancreas	Pancrea
49	chr4:99802800-99830200	Weak transcription	Ovary	ovary
50	chr4:99802800-99849000	Weak transcription	Aorta	Aorta

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